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<DIV><FONT size=2 face=Arial><SPAN class=834524411-25052010>Dear
Justin,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=834524411-25052010>to add other
elements to find a solution to this problem, </SPAN></FONT><FONT size=2
face=Arial><SPAN class=834524411-25052010>I repeated all the Gromacs procedure
until minimization on the file PDB I used as template to model my protein.
pdb2gmx warns that 232 atoms have non-zero occupancy, it's because there are
sidechains with alternative conformations, but for the rest everything is OK.
When I try to launch the mdrun to minimize the protein, however, the range
checking error appears:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=834524411-25052010></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=834524411-25052010>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman">Reading file 1WBE_min.tpr, VERSION 4.0.7 (double
precision)<?xml:namespace prefix = o ns =
"urn:schemas-microsoft-com:office:office" /><o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman">Steepest Descents:<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman"><SPAN style="mso-spacerun: yes">
</SPAN>Tolerance (Fmax)<SPAN style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>1.00000e+03<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman"><SPAN style="mso-spacerun: yes">
</SPAN>Number of steps<SPAN style="mso-spacerun: yes">
</SPAN>=<SPAN
style="mso-spacerun: yes">
</SPAN>50000<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><o:p><FONT size=3
face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman">-------------------------------------------------------<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman">Program mdrun_d, VERSION
4.0.7<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman">Source code file: nsgrid.c, line:
357<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><o:p><FONT size=3
face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman">Range checking error:<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman">Explanation: During neighborsearching, we assign each
particle to a grid<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman">based on its coordinates. If your system contains
collisions or parameter<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman">errors that give particles very high velocities you might
end up with some<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman">coordinates being +-Infinity or NaN (not-a-number).
Obviously, we cannot<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman">put these on a grid, so this is usually where we detect
those errors.<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman">Make sure your system is properly energy-minimized and
that the potential<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman">energy seems reasonable before trying
again.<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><o:p><FONT size=3
face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman">Variable ci has value -2147483648. It should have been
within [ 0 .. 1728 ]</FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face="Times New Roman"></FONT></FONT></SPAN> </P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><o:p><SPAN
class=834524411-25052010>So I think definitely that the problem is in the
protein structure arising from some bad coordinates in the template I used to
model my protein.</SPAN></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><o:p><SPAN
class=834524411-25052010>I have to wait for the approval of people working on
this project to send you coordinates and topologies of my model, but since I
think that the error in the model is strictly derived from the error in this
public file, I will send you privately the coordinates and topologies of this
file. Please remember that in my model there are some atoms with occupancy
<1, but the conformation of the sidechains is unique. I corrected by hand the
occupancy on my model, re-tried to minimize it and nothing changed: the same
error occurs. On the contrary, in this case, with this template
file, the mdrun did not start at all.</SPAN></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><o:p><SPAN
class=834524411-25052010></SPAN></o:p></SPAN> </P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><o:p><SPAN
class=834524411-25052010>Once again thank you very much and best
regards</SPAN></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><o:p><SPAN
class=834524411-25052010>Anna</SPAN></o:p></SPAN></P></SPAN></FONT></DIV>
<DIV> </DIV>
<DIV align=left><FONT size=2
face=Arial>____________________________________________________</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Anna Marabotti, Ph.D.</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Laboratory of Bioinformatics and
Computational Biology</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Institute of Food Science,
CNR</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Via Roma, 64</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>83100 Avellino (Italy)</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Phone: +39 0825 299651</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Fax: +39 0825 781585</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Email: <A
href="mailto:anna.marabotti@isa.cnr.it">anna.marabotti@isa.cnr.it</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Skype account: annam1972</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Web page: <A
href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial></FONT> </DIV>
<DIV align=left><FONT size=2 face=Arial>"If you think you are too small to make
a difference, try sleeping with a mosquito"</FONT></DIV>
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